Laboratory and field data showed that deep mixed (DM) columns accelerated the rate of consolidation of the soft foundations. Most analyses of consolidation of DM column-improved foundations so far have been based on the elastic theory. In reality, the DM columns may yield due to the stress concentration from the soft soil and its limited strength. The influence of column yielding on the degree of consolidation of the soft foundation improved by DM columns has not been well investigated. A three-dimensional mechanically and hydraulically-coupled numerical method was adopted in this study to investigate the degree of consolidation of the DM column foundation considering column yielding. A unit cell model was used, in which the soil was modeled as a linearly elastic material. For a comparison purpose, the DM column was modeled as an elastic or elastic-plastic material. This study examined the aspects of stress transfer, settlement, and degree of consolidation of the foundations without or with the consideration of the yielding of the DM column. A parametric study was conducted to investigate the influence of the column yielding on the stress concentration ratio, settlement, and average degree of consolidation of the DM column foundation. The stress concentration ratio increased and then decreased to reach a constant value with the increase of the column modulus and time. A simplified method was proposed to calculate the maximum stress concentration ratios under undrained and drained conditions considering the column yielding. The simplified method based on a composite foundation concept could conservatively estimate the consolidation settlement. An increase of the column modulus, area replacement ratio, and/or column permeability increased the rate of consolidation.